Immunogenic proteins against Clostridium difficile

ABSTRACT

Described are immunogenic proteins against  Clostridium difficile . Also described are compositions comprising the immunogenic proteins. Further described are methods of preventing or treating a  Clostridium difficile  infection in a subject in need thereof.

CROSS-REFERENCE TO RELATED APPLICATION(S)

This application is a continuation application of U.S. patent application Ser. No. 15/992,497, filed on May 30, 2018, which claims priority to U.S. Provisional Patent Application No. 62/513,247, filed on May 31, 2017, the entire contents of which are fully incorporated herein by reference.

STATEMENT OF GOVERNMENT SUPPORT

This invention was made with government support under Grant Numbers R21 AI113470 and K01 DK092352 awarded by the National Institutes of Health. The government has certain rights in the invention.

INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED ELECTRONICALLY

Incorporated by reference in its entirety herein is a computer-readable nucleotide/amino acid sequence listing submitted concurrently herewith and identified as follows: One 64,312 Bytes ASCII (Text) file named “17A057PRC-210112-9062-US02_ST25.txt”, created on May 29, 2018.

TECHNICAL FIELD

The present disclosure relates to immunogenic proteins and methods for treating and/or preventing infections caused by Clostridium difficile.

BACKGROUND

Clostridium difficile is a spore-forming anaerobic and toxin-producing bacillus. It is the most common cause of nosocomial antibiotic-associated diarrhea. A CDC study estimated that 29,000 deaths were caused by Clostridium difficile in the U.S. in 2011. Antibiotic treatment of Clostridium difficile infections may be difficult, due both to antibiotic resistance and physiological factors of the bacteria (e.g., spore formation and protective effects of the pseudomembrane). Accordingly, there exists a need for effective therapies and prevention of infections caused by Clostridium difficile.

SUMMARY OF THE INVENTION

In one aspect, disclosed is an immunogenic protein that comprises the glucosyltranferase domain of Clostridium difficile toxin TcdB, the cysteine proteinase domain of Clostridium difficile toxin TcdB, and the receptor binding domain of Clostridium difficile toxin TcdA. Also disclosed is an immunogenic protein comprising the glucosyltranferase domain of Clostridium difficile toxin TcdB, the cysteine proteinase domain of Clostridium difficile toxin TcdB, the receptor binding domain of Clostridium difficile toxin TcdA, and the receptor binding domain of Clostridium difficile toxin TcdB. Also disclosed is an immunogenic protein comprising the glucosyltranferase domain of Clostridium difficile toxin TcdB, the cysteine proteinase domain of Clostridium difficile toxin TcdB, the receptor binding domain of Clostridium difficile toxin TcdA, the receptor binding domain of Clostridium difficile toxin TcdB, and Salmonella typhimurium flagellin. Also disclosed is an immunogenic protein comprising the glucosyltranferase domain of Clostridium difficile toxin TcdB, the cysteine proteinase domain of Clostridium difficile toxin TcdB, and the receptor binding domain of Clostridium difficile toxin TcdA, and Salmonella typhimurium flagellin. The immunogenic proteins may comprise a W102A amino acid substitution and a D288N amino acid substitution in the glucosyltransferase domain. The immunogenic proteins may comprise a C698A amino acid substitution in the cysteine proteinase domain. The disclosed immunogenic proteins may lack a transmembrane domain.

Further disclosed are compositions comprising the disclosed immunogenic proteins against Clostridium difficile. Also disclosed are methods of treating Clostridium difficile bacterial infection in a subject. The method may comprise administering to the subject an effective amount of the disclosed immunogenic proteins or compositions comprising the same.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1D show the domains of TcdA and TcdB and construction of Tcd169, Tcd169Fl, and Tcd138Fl. Brackets are used to indicate domains that are connected by a GGSG linker (SEQ ID NO: 1). FIG. 1A shows the domains of TcdA and TcdB. FIG. 1B shows construction of Tcd169 (SEQ ID NO: 5), of which the GT of TcdB and the CPD of TcdB (SEQ ID NO: 8), the RBD of TcdB (SEQ ID NO: 10) and the RBD of TcdA (SEQ ID NO: 9) are connected by GGSG linkers. FIG. 1C shows construction of Tcd169Fl (SEQ ID NO: 6), of which the GT of TcdB and the CPD of TcdB (SEQ ID NO: 8), the RBD of TcdB (SEQ ID NO: 10), the RBD of TcdA (SEQ ID NO: 9) and the sFLiC (SEQ ID NO: 11) are connected by GGSG linkers. FIG. 1D shows construction of Tcd138Fl (SEQ ID NO: 7), of which the GT of TcdB and the CPD of TcdB (SEQ ID NO: 8), the RBD of TcdA (SEQ ID NO: 9) and the sFLiC (SEQ ID NO: 11) are connected by GGSG linkers.

FIG. 2 shows the expression and purification of Tcd169.

FIG. 3 shows the expression and purification of Tcd169Fl.

FIG. 4 shows the expression and purification of Clostridium difficile Cwp84 protein.

FIG. 5 shows the toxin gene profiles of two selected Clostridium difficile strains. Lane 1, tcdA⁺, tcdB⁺; Lane 2, non-toxigenic C. difficile; Lane M: 100-bp DNA marker. A rapid 3-plex PCR was developed for the detection of tcdA, tcdB and 16s rDNA. 5 μl of 12-24 hrs of Clostridium difficile culture was used as template.

FIG. 6 shows the colonic inflammation and injury caused by direct intra-rectal instillation of TcdA/TcdB. A 5F infant feeding tube was inserted 2.5 cm up the colon. 100 μl of TcdA (10 μg)+TcdB (10 μg) or PBS was slowly administered. 4 or 5 hours later mice were euthanized and dissected to analyze the toxin-mediated effects on the colon.

FIGS. 7A-7B show immunization and challenge schemes for CDI relapse models in mice. After 3 immunizations mice may be pretreated with antibiotic mixture, challenged with Clostridium difficile UK6 spores, and monitored for about a week. Thirty days after initial spore challenge, survived mice may be again treated with antibiotics mixture followed by infection with Clostridium difficile UK6 spores and monitoring (FIG. 7A). Non-immunized naïve mice may be pretreated with antibiotic mixture, challenged with Clostridium difficile UK6 spores, and monitored for about a week. Starting on post-infection day 5, mice may be immunized for 3 times at 10-day intervals. Ten days after third immunization, mice may be again treated with antibiotics mixture followed by infection with Clostridium difficile UK6 spores and monitoring (FIG. 7B).

FIGS. 8A-8E show the protective responses of Tcd169 immunization (IM or IP) in mice. Groups of C57 BL/6 mice (n=10) were immunized with Tcd169 (10 μg) or PBS in the presence of alum for 3 times at 14-day intervals (IM or IP). Anti-toxin IgG titers (FIG. 8A) and anti-toxin neutralizing titers (FIG. 8B, FIG. 8C) in sera from third immunization were measured. Seven days after third immunization, mice were given antibiotic mixture in drinking water for 4 days, switched to regular water for 2 days, and were given one dose of clindamycin (10 mg/kg) one day before infection with 10⁶ of Clostridium difficile UK6 spores by gavage. After infection, mouse survivals (P=0.0486 between PBS and Tcd169 IM/Tcd169 IP groups) (FIG. 9D), and mean relative weight changes (FIG. 8E) of different groups were recorded. The neutralizing titer is expressed as the maximum dilution of the sera that inhibits Vero cell rounding caused by toxin at a given concentration. This given concentration is the minimum toxin dose causing cell rounding after a 16 h of toxin exposure, i.e., 2.5 and 0.1 ng/ml for TcdA and TcdB, respectively.

FIGS. 9A-9F show that intramuscular immunization of mice with Tcd169Fl induces potent anti-toxin/sFliC responses. Groups of C57 BL/6 mice (n=10) were immunized with Tcd169Fl (10 μg) or PBS in the presence of alum for 3 times at 14-day intervals (IM). IgG titers against TcdA (FIG. 9A), TcdB (FIG. 9B), or sFliC (FIG. 9C), and IgA titers against TcdA (FIG. 9D), TcdB (FIG. 9E), or sFliC (FIG. 9F) were determined.

FIGS. 10A-10C show that immunization with Tcd169Fl provides mice full protection against infection with hypervirulent Clostridium difficile UK1. Seven days after third immunization with Tcd169Fl, mice were given antibiotic mixture in drinking water for 4 days, switched to regular water for 2 days, and were given one dose of clindamycin (10 mg/kg) one day before infection with 10⁶ of Clostridium difficile UK1 spores by gavage. After infection, mouse survivals (P=0.0486 between PBS and Tcd169Fl) (FIG. 10A), mean relative weight changes (FIG. 10B) and percent diarrhea (FIG. 10C) of different groups were recorded.

FIG. 11 shows the nucleotide sequence that encodes for Tcd169 (4251 bp) (SEQ ID NO.: 2).

FIG. 12 shows the nucleotide sequence that encodes for Tcd169Fl (5745 bp) (SEQ ID NO.: 3).

FIG. 13 shows the nucleotide sequence that encodes for Tcd138Fl (5124 bp) (SEQ ID NO.: 4).

FIG. 14 shows the amino acid sequence for Tcd169 (SEQ ID NO.: 5).

FIG. 15 shows the amino acid sequence for Tcd169Fl (SEQ ID NO.: 6).

FIG. 16 shows the amino acid sequence for Tcd138Fl (SEQ ID NO.: 7).

DETAILED DESCRIPTION

Disclosed herein are immunogenic proteins and compositions useful for the treatment or prevention of bacterial infections. The bacterial infection may be caused by Clostridium difficile. The disclosed immunogenic proteins and compositions may be used to prevent a Clostridium difficile infection in a subject. The disclosed immunogenic proteins and compositions may be used to treat a Clostridium difficile infection in a subject. Methods of treating and/or preventing a Clostridium difficile infection are disclosed.

1. DEFINITIONS

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. In case of conflict, the present document, including definitions, will control. Preferred methods and materials are described below, although methods and materials similar or equivalent to those described herein can be used in practice or testing of the present invention. All publications, patent applications, patents and other references mentioned herein are incorporated by reference in their entirety. The materials, methods, and examples disclosed herein are illustrative only and not intended to be limiting.

The modifier “about” used in connection with a quantity is inclusive of the stated value and has the meaning dictated by the context (for example, it includes at least the degree of error associated with the measurement of the particular quantity). The modifier “about” should also be considered as disclosing the range defined by the absolute values of the two endpoints. For example, the expression “from about 2 to about 4” also discloses the range “from 2 to 4.” The term “about” may refer to plus or minus 10% of the indicated number. For example, “about 10%” may indicate a range of 9% to 11%, and “about 1” may mean from 0.9-1.1. Other meanings of “about” may be apparent from the context, such as rounding off, so, for example “about 1” may also mean from 0.5 to 1.4.

The terms “administration” or “administering” as used herein may include the process in which the immunogenic proteins and compositions as described herein are delivered to a subject. The immunogenic proteins and compositions may be administered in various routes including, but not limited to, oral, mucosal, mucosal nasal, parenteral (including intravenous, intra-arterial, and other appropriate parenteral routes), intrathecally, intramuscularly, subcutaneously, colonically, rectally, and nasally, transcutaneously, among others. The dosing of the immunogenic proteins and compositions described may be determined by the circumstances of the subject, as known in the art. The dosing of a subject herein may be accomplished through individual or unit doses of the immunogenic proteins and compositions herein or by a combined or prepackaged or pre-formulated dose.

Administration may depend upon the amount of immunogenic protein or composition administered, the number of doses, duration of treatment, and the like. For example, multiple doses of the immunogenic protein or composition may be administered to the subject. The frequency of administration of the immunogenic protein or composition may vary depending on any of a variety of factors. The duration of administration of the immunogenic protein or composition, e.g., the period of time over which the immunogenic protein or composition is administered, may vary, depending on any of a variety of factors, including subject response, etc.

The amount of the immunogenic proteins and compositions administered may vary according to factors such as the degree of susceptibility of the individual, the age, sex, and weight of the individual, idiosyncratic responses of the individual, the dosimetry, and the like. Detectably effective amounts of the immunogenic protein or composition of the present disclosure may also vary.

As used in this specification and the appended claims, the singular forms “a”, “an”, and “the” include plural referents unless the content clearly dictates otherwise. As used in this specification and the appended claims, the term “or” is generally employed in its sense including “and/or” unless the context clearly dictates otherwise.

The terms “Clostridium difficile”, “C. difficile, C. diff”, and “CDF”, and “cdf” as used herein, may be used interchangeably.

The terms “comprise(s),” “include(s),” “having,” “has,” “can,” “contain(s),” and variants thereof, as used herein, are intended to be open-ended transitional phrases, terms, or words that do not preclude the possibility of additional acts or structures. The singular forms “a,” “an” and “the” include plural references unless the context clearly dictates otherwise. The present disclosure also contemplates other embodiments “comprising,” “consisting of” and “consisting essentially of,” the embodiments or elements presented herein, whether explicitly set forth or not.

The terms “composition”, “compositions”, “pharmaceutical composition”, and “pharmaceutical compositions” are used interchangeably herein to refer to a composition comprising an immunogenic protein disclosed herein.

The term “immunogen”, as used herein refers to any substance that may be specifically bound by components of the immune system.

The term “parenterally,” as used herein, refers to modes of administration which include intravenous, intramuscular, intraperitoneal, intrasternal, subcutaneous and intraarticular injection and infusion.

A “pharmaceutically acceptable excipient,” “pharmaceutically acceptable diluent,” “pharmaceutically acceptable carrier,” or “pharmaceutically acceptable adjuvant” means an excipient, diluent, carrier, and/or adjuvant that are useful in preparing a pharmaceutical composition that are generally safe, non-toxic and neither biologically nor otherwise undesirable, and includes an excipient, diluent, carrier, and adjuvant that are acceptable for veterinary use and/or human pharmaceutical use.

As used herein, the term “subject,” “patient,” or “organism” includes humans and mammals (e.g., mice, rats, pigs, cats, dogs, and horses). Typical subjects to which an agent(s) of the present disclosure may be administered may include mammals, particularly primates, especially humans. For veterinary applications, suitable subjects may include, for example, livestock such as cattle, sheep, goats, cows, swine, and the like; poultry such as chickens, ducks, geese, turkeys, and the like; and domesticated animals particularly pets such as dogs and cats. For diagnostic or research applications, suitable subjects may include mammals, such as rodents (e.g., mice, rats, hamsters), rabbits, primates, and swine such as inbred pigs and the like. The subject may have a bacterial infection. The subject may have a bacterial infection caused by Clostridium difficile. The subject may be taking antibiotics. The subject may be taking antibiotics for a bacterial infection that is caused by bacteria other than Clostridium difficile. The subject may be at risk for an infection caused by Clostridium difficile.

A “therapeutically effective amount” or “effective amount” as used interchangeably herein, refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic result. A therapeutically effective amount of the immunogenic protein or composition may be determined by a person skilled in the art and may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the composition to elicit a desired response in the individual. A therapeutically effective amount is also one in which any toxic or detrimental effects of immunogenic proteins and compositions of the disclosure are outweighed by the therapeutically beneficial effects. The term “toxin” as used herein, may refer to small molecules, peptides, or proteins that are capable of causing disease on contact with or absorption by body tissues interacting with biological macromolecules such as enzymes or cellular receptors. Toxins may be produced by microorganisms. Toxins may be produced by Clostridium difficile. Toxins may be virulence determinants responsible for microbial pathogenicity. Toxins may be virulence determinants responsible for evasion of the host immune response.

“Treat,” “treatment,” or “treating,” means preventing, suppressing, repressing, ameliorating, or completely eliminating a pathological condition. For example, the pathological condition may be a bacterial infection caused by Clostridium difficile. Preventing the pathological condition involves administering an immunogenic protein or composition of the present invention to a subject prior to onset of the pathological condition. For example, preventing Clostridium difficile infection may involve administering the immunogenic protein or composition of the present invention to a subject prior to onset of the infection. Repressing or ameliorating the pathological condition involves administering an immunogenic protein or composition of the present invention to a subject after clinical appearance of the pathological condition. For example, repressing or ameliorating Clostridium difficile infection may involve administering an immunogenic protein or composition of the present invention after onset of symptoms of Clostridium difficile infection. Administration of the immunogenic proteins or compositions of the present invention may improve or prevent one or more symptoms associated with the pathological condition. For example, administration of the immunogenic proteins or compositions of the present invention may improve or prevent one or more symptoms associated with Clostridium difficile infection. Symptoms include, but are not limited to, watery diarrhea, fever, loss of appetite, nausea, abdominal pain/tenderness.

For the recitation of numeric ranges herein, each intervening number there between with the same degree of precision is explicitly contemplated. For example, for the range of 6-9, the numbers 7 and 8 are contemplated in addition to 6 and 9, and for the range 6.0-7.0, the number 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, and 7.0 are explicitly contemplated.

2. IMMUNOGENIC PROTEINS AGAINST CLOSTRIDIUM DIFFICILE

In one aspect, disclosed are immunogenic proteins against Clostridium difficile. The immunogenic protein may be a chimeric protein. The immunogenic protein may comprise one or more domains from Clostridium difficile toxins. The immunogenic protein may comprise one or more domains from Clostridium difficile toxin A (TcdA). The immunogenic protein may comprise the glucosyltransferase domain (GT) from TcdA. The immunogenic protein may comprise the cysteine proteinase domain (CPD) from TcdA. The immunogenic protein may comprise the receptor binding domain (RBD) from TcdA. The immunogenic protein may contain one or more domains from Clostridium difficile toxin B (TcdB). The immunogenic protein may comprise the glucosyltransferase domain from TcdB. The immunogenic protein may comprise the cysteine proteinase domain from TcdB. The immunogenic protein may comprise the receptor binding domain from TcdB. The immunogenic protein may lack a transmembrane domain.

The immunogenic protein may contain one or more domains from Salmonella typhimurium. The immunogenic protein may contain Salmonella typhimurium flagellin. For example, the immunogenic protein may contain sFliC.

The one or more domains may be connected by an amino acid linker. Any combination of one or more domains may be connected by an amino acid linker. For example, the CPD of TcdB and the RBD of TcdB may be connected by an amino acid linker. As another example, the CPD of TcdB and the RBD of TcdA may be connected by an amino acid linker. The RBD of TcdB and the RBD of TcdA may be connected by an amino acid linker. The TBD of TcdA and sFliC may be connected by an amino acid linker. The amino acid linker may be the amino acid sequence GGSG as set forth in SEQ ID NO.: 1.

The immunogenic proteins may comprise one or more mutations. The one or more mutations may reduce the toxicity of the immunogenic protein. The one or more mutations may render the immunogenic protein atoxic. For example, the immunogenic protein may comprise one or more amino acid substitutions. For example, the immunogenic protein may comprise a W102A amino acid substitution and a D288N amino acid substitution in the GT of TcdB. The immunogenic protein may comprise a C698A amino acid substitution in the CPD of TcdB. The immunogenic protein may comprise a W102A amino acid substitution and a D288N amino acid substitution in the GT of TcdB and a C698A amino acid substitution in the CPD of TcdB.

The immunogenic protein may comprise the glucosyltransferase domain of TcdB, cysteine proteinase domain of TcdB, receptor binding domain of TcdB, and the receptor binding domain of TcdA. The immunogenic protein may comprise a W102A amino acid substitution and a D288N amino acid substitution in the GT of TcdB. The immunogenic protein may comprise a C698A amino acid substitution in the CPD of TcdB. The immunogenic protein may comprise a W102A amino acid substitution and a D288N amino acid substitution in the GT of TcdB and a C698A amino acid substitution in the CPD of TcdB. The immunogenic protein may be encoded by the nucleotide sequence as set forth in SEQ ID NO.: 2. The immunogenic protein may be Tcd169 (SEQ ID NO.: 5).

The immunogenic protein may comprise the glucosyltransferase domain of TcdB, cysteine proteinase domain of TcdB, receptor binding domain of TcdB, the receptor binding domain of TcdA, and flagellin of Salmonella typhimurium. The immunogenic protein may comprise a W102A amino acid substitution and a D288N amino acid substitution in the GT of TcdB. The immunogenic protein may comprise a C698A amino acid substitution in the CPD of TcdB. The immunogenic protein may comprise a W102A amino acid substitution and a D288N amino acid substitution in the GT of TcdB and a C698A amino acid substitution in the CPD of TcdB. The immunogenic protein may be encoded by the nucleotide sequence as set forth in SEQ ID NO.: 3. The immunogenic protein may be Tcd169Fl (SEQ ID NO: 6).

In some embodiments, the immunogenic protein comprises the glucosyltransferase domain of TcdB, the cysteine proteinase domain of TcdB, the receptor binding domain (RBD) of TcdA, and flagellin of Salmonella typhimurium. The immunogenic protein may comprise a W102A amino acid substitution and a D288N amino acid substitution in the GT of TcdB. The immunogenic protein may comprise a C698A amino acid substitution in the CPD of TcdB. The immunogenic protein may comprise a W102A amino acid substitution and a D288N amino acid substitution in the GT of TcdB and a C698A amino acid substitution in the CPD of TcdB. The immunogenic protein may be encoded by the nucleotide sequence as set forth in SEQ ID NO.: 4. The immunogenic protein may be Tcd138Fl (SEQ ID NO.: 7).

The immunogenic proteins may induce a humoral immune response. The immunogenic proteins may induce a cell-mediated immune response.

3. PHARMACEUTICAL COMPOSITIONS

The disclosed immunogenic proteins may be incorporated into pharmaceutical compositions suitable for administration to a subject. The pharmaceutical composition may include a therapeutically effective amount of the immunogenic protein. For example, a therapeutically effective amount of the immunogenic protein may be about 1 mg/kg to about 1000 mg/kg, about 5 mg/kg to about 950 mg/kg, about 10 mg/kg to about 900 mg/kg, about 15 mg/kg to about 850 mg/kg, about 20 mg/kg to about 800 mg/kg, about 25 mg/kg to about 750 mg/kg, about 30 mg/kg to about 700 mg/kg, about 35 mg/kg to about 650 mg/kg, about 40 mg/kg to about 600 mg/kg, about 45 mg/kg to about 550 mg/kg, about 50 mg/kg to about 500 mg/kg, about 55 mg/kg to about 450 mg/kg, about 60 mg/kg to about 400 mg/kg, about 65 mg/kg to about 350 mg/kg, about 70 mg/kg to about 300 mg/kg, about 75 mg/kg to about 250 mg/kg, about 80 mg/kg to about 200 mg/kg, about 85 mg/kg to about 150 mg/kg, and about 90 mg/kg to about 100 mg/kg.

The pharmaceutical composition may further comprise one or more Clostridium difficile immunogens. For example, the composition may further comprise one or more Clostridium difficile surface proteins. For example, the composition may comprise Cwp84.

The pharmaceutical composition may include one or more pharmaceutically acceptable carriers. Some examples of materials which can serve as pharmaceutically acceptable carriers are sugars such as, but not limited to, lactose, glucose and sucrose; starches such as, but not limited to, corn starch and potato starch; cellulose and its derivatives such as, but not limited to, sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients such as, but not limited to, cocoa butter and suppository waxes; oils such as, but not limited to, peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; glycols; such as propylene glycol; esters such as, but not limited to, ethyl oleate and ethyl laurate; agar; buffering agents such as, but not limited to, magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline; Ringer's solution; ethyl alcohol, and phosphate buffer solutions, as well as other non-toxic compatible lubricants such as, but not limited to, sodium lauryl sulfate and magnesium stearate, as well as coloring agents, releasing agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants can also be present in the composition, according to the judgment of the formulator.

The route by which the disclosed pharmaceutical compositions are administered and the form of the pharmaceutical composition will dictate the type of carrier to be used. The pharmaceutical composition may be in a variety of forms, suitable, for example, for systemic administration (e.g., oral, rectal, nasal, sublingual, buccal, implants, or parenteral) or topical administration (e.g., dermal, pulmonary, nasal, aural, ocular, liposome delivery systems, transdermal, or iontophoresis).

Carriers for systemic administration typically include at least one of diluents, lubricants, binders, disintegrants, colorants, flavors, sweeteners, antioxidants, preservatives, glidants, solvents, suspending agents, wetting agents, surfactants, combinations thereof, and others. All carriers are optional in the compositions.

Suitable diluents include sugars such as glucose, lactose, dextrose, and sucrose; diols such as propylene glycol; calcium carbonate; sodium carbonate; sugar alcohols, such as glycerin; mannitol; and sorbitol. The amount of diluent(s) in a systemic or topical composition is typically about 50 to about 90%.

Suitable lubricants include silica, talc, stearic acid and its magnesium salts and calcium salts, calcium sulfate; and liquid lubricants such as polyethylene glycol and vegetable oils such as peanut oil, cottonseed oil, sesame oil, olive oil, corn oil and oil of theobroma. The amount of lubricant(s) in a systemic or topical composition is typically about 5 to about 10%.

Suitable binders include polyvinyl pyrrolidone; magnesium aluminum silicate; starches such as corn starch and potato starch; gelatin; tragacanth; and cellulose and its derivatives, such as sodium carboxymethylcellulose, ethyl cellulose, methylcellulose, microcrystalline cellulose, and sodium carboxymethylcellulose. The amount of binder(s) in a systemic composition is typically about 5 to about 50%.

Suitable disintegrants include agar, alginic acid and the sodium salt thereof, effervescent mixtures, croscarmelose, crospovidone, sodium carboxymethyl starch, sodium starch glycolate, clays, and ion exchange resins. The amount of disintegrant(s) in a systemic or topical composition is typically about 0.1 to about 10%.

Suitable colorants include a colorant such as an FD&C dye. When used, the amount of colorant in a systemic or topical composition is typically about 0.005 to about 0.1%.

Suitable flavors include menthol, peppermint, and fruit flavors. The amount of flavor(s), when used, in a systemic or topical composition is typically about 0.1 to about 1.0%.

Suitable sweeteners include aspartame and saccharin. The amount of sweetener(s) in a systemic or topical composition is typically about 0.001 to about 1%.

Suitable antioxidants include butylated hydroxyanisole (“BHA”), butylated hydroxytoluene (“BHT”), and vitamin E. The amount of antioxidant(s) in a systemic or topical composition is typically about 0.1 to about 5%.

Suitable preservatives include benzalkonium chloride, methyl paraben and sodium benzoate. The amount of preservative(s) in a systemic or topical composition is typically about 0.01 to about 5%.

Suitable glidants include silicon dioxide. The amount of glidant(s) in a systemic or topical composition is typically about 1 to about 5%.

Suitable solvents include water, isotonic saline, ethyl oleate, glycerine, hydroxylated castor oils, alcohols such as ethanol, and phosphate buffer solutions. The amount of solvent(s) in a systemic or topical composition is typically from about 0 to about 100%.

Suitable suspending agents include AVICEL RC-591 (from FMC Corporation of Philadelphia, Pa.) and sodium alginate. The amount of suspending agent(s) in a systemic or topical composition is typically about 1 to about 8%.

Suitable surfactants include lecithin, Polysorbate 80, and sodium lauryl sulfate, and the TWEENS from Atlas Powder Company of Wilmington, Del. Suitable surfactants include those disclosed in the C.T.F.A. Cosmetic Ingredient Handbook, 1992, pp. 587-592; Remington's Pharmaceutical Sciences, 15th Ed. 1975, pp. 335-337; and McCutcheon's Volume 1, Emulsifiers & Detergents, 1994, North American Edition, pp. 236-239. The amount of surfactant(s) in the systemic or topical composition is typically about 0.1% to about 5%.

Although the amounts of components in the systemic compositions may vary depending on the type of systemic composition prepared, in general, systemic compositions include 0.01% to 50% of active and 50% to 99.99% of one or more carriers. Compositions for parenteral administration typically include 0.1% to 10% of actives and 90% to 99.9% of a carrier including a diluent and a solvent.

Compositions for oral administration can have various dosage forms. For example, solid forms include tablets, capsules, granules, and bulk powders. These oral dosage forms include a safe and effective amount, usually at least about 5%, and more particularly from about 25% to about 50% of actives. The oral dosage compositions include about 50% to about 95% of carriers, and more particularly, from about 50% to about 75%.

Tablets can be compressed, tablet triturates, enteric-coated, sugar-coated, film-coated, or multiple-compressed. Tablets typically include an active component, and a carrier comprising ingredients selected from diluents, lubricants, binders, disintegrants, colorants, flavors, sweeteners, glidants, and combinations thereof. Specific diluents include calcium carbonate, sodium carbonate, mannitol, lactose and cellulose. Specific binders include starch, gelatin, and sucrose. Specific disintegrants include alginic acid and croscarmelose. Specific lubricants include magnesium stearate, stearic acid, and talc. Specific colorants are the FD&C dyes, which can be added for appearance. Chewable tablets preferably contain sweeteners such as aspartame and saccharin, or flavors such as menthol, peppermint, fruit flavors, or a combination thereof.

Capsules (including implants, time release and sustained release formulations) typically include an active compound, and a carrier including one or more diluents disclosed above in a capsule comprising gelatin. Granules typically comprise a disclosed compound, and preferably glidants such as silicon dioxide to improve flow characteristics. Implants can be of the biodegradable or the non-biodegradable type.

The selection of ingredients in the carrier for oral compositions depends on secondary considerations like taste, cost, and shelf stability, which are not critical for the purposes of this invention.

Solid compositions may be coated by conventional methods, typically with pH or time-dependent coatings, such that a disclosed compound is released in the gastrointestinal tract in the vicinity of the desired application, or at various points and times to extend the desired action. The coatings typically include one or more components selected from the group consisting of cellulose acetate phthalate, polyvinyl acetate phthalate, hydroxypropyl methyl cellulose phthalate, ethyl cellulose, EUDRAGIT coatings (available from Rohm & Haas G.M.B.H. of Darmstadt, Germany), waxes and shellac.

Compositions for oral administration can have liquid forms. For example, suitable liquid forms include aqueous solutions, emulsions, suspensions, solutions reconstituted from non-effervescent granules, suspensions reconstituted from non-effervescent granules, effervescent preparations reconstituted from effervescent granules, elixirs, tinctures, syrups, and the like. Liquid compositions, which may be administered orally, may include a disclosed immunogenic proteins and a carrier, namely, a carrier selected from diluents, colorants, flavors, sweeteners, preservatives, solvents, suspending agents, and surfactants. Peroral liquid compositions preferably include one or more ingredients selected from colorants, flavors, and sweeteners.

Other compositions useful for attaining systemic delivery of the subject compounds include sublingual, buccal and nasal dosage forms. Such compositions typically include one or more of soluble filler substances such as diluents including sucrose, sorbitol and mannitol; and binders such as acacia, microcrystalline cellulose, carboxymethyl cellulose, and hydroxypropyl methylcellulose. Such compositions may further include lubricants, colorants, flavors, sweeteners, antioxidants, and glidants.

The disclosed immunogenic proteins and compositions may be topically administered. Topical compositions that can be applied locally to the skin may be in any form including solids, solutions, oils, creams, ointments, gels, lotions, shampoos, leave-on and rinse-out hair conditioners, milks, cleansers, moisturizers, sprays, skin patches, and the like. The carrier of the topical composition preferably aids penetration of the compounds into the skin. The carrier may further include one or more optional components. Transdermal administration may be used to facilitate delivery.

The amount of the carrier employed in conjunction with a disclosed compound is sufficient to provide a practical quantity of composition for administration per unit dose of the medicament. Techniques and compositions for making dosage forms useful in the methods of this invention are described in the following references: Modern Pharmaceutics, Chapters 9 and 10, Banker & Rhodes, eds. (1979); Lieberman et al., Pharmaceutical Dosage Forms: Tablets (1981); and Ansel, Introduction to Pharmaceutical Dosage Forms, 2nd Ed., (1976).

A carrier may include a single ingredient or a combination of two or more ingredients. In the topical compositions, the carrier includes a topical carrier. Suitable topical carriers include one or more ingredients selected from phosphate buffered saline, isotonic water, deionized water, monofunctional alcohols, symmetrical alcohols, aloe vera gel, allantoin, glycerin, vitamin A and E oils, mineral oil, propylene glycol, PPG-2 myristyl propionate, dimethyl isosorbide, castor oil, combinations thereof, and the like. More particularly, carriers for skin applications include propylene glycol, dimethyl isosorbide, and water, and even more particularly, phosphate buffered saline, isotonic water, deionized water, monofunctional alcohols, and symmetrical alcohols.

The carrier of a topical composition may further include one or more ingredients selected from emollients, propellants, solvents, humectants, thickeners, powders, fragrances, pigments, and preservatives, all of which are optional.

Suitable emollients include stearyl alcohol, glyceryl monoricinoleate, glyceryl monostearate, propane-1,2-diol, butane-1,3-diol, mink oil, cetyl alcohol, isopropyl isostearate, stearic acid, isobutyl palmitate, isocetyl stearate, oleyl alcohol, isopropyl laurate, hexyl laurate, decyl oleate, octadecan-2-ol, isocetyl alcohol, cetyl palmitate, di-n-butyl sebacate, isopropyl myristate, isopropyl palmitate, isopropyl stearate, butyl stearate, polyethylene glycol, triethylene glycol, lanolin, sesame oil, coconut oil, arachis oil, castor oil, acetylated lanolin alcohols, petroleum, mineral oil, butyl myristate, isostearic acid, palmitic acid, isopropyl linoleate, lauryl lactate, myristyl lactate, decyl oleate, myristyl myristate, and combinations thereof. Specific emollients for skin include stearyl alcohol and polydimethylsiloxane. The amount of emollient(s) in a skin-based topical composition is typically about 5% to about 95%.

Suitable propellants include propane, butane, isobutane, dimethyl ether, carbon dioxide, nitrous oxide, and combinations thereof. The amount of propellant(s) in a topical composition is typically about 0% to about 95%.

Suitable solvents include water, ethyl alcohol, methylene chloride, isopropanol, castor oil, ethylene glycol monoethyl ether, diethylene glycol monobutyl ether, diethylene glycol monoethyl ether, dimethylsulfoxide, dimethyl formamide, tetrahydrofuran, and combinations thereof. Specific solvents include ethyl alcohol and homotopic alcohols. The amount of solvent(s) in a topical composition is typically about 0% to about 95%.

Suitable humectants include glycerin, sorbitol, sodium 2-pyrrolidone-5-carboxylate, soluble collagen, dibutyl phthalate, gelatin, and combinations thereof. Specific humectants include glycerin. The amount of humectant(s) in a topical composition is typically 0% to 95%.

The amount of thickener(s) in a topical composition is typically about 0% to about 95%.

Suitable powders include beta-cyclodextrins, hydroxypropyl cyclodextrins, chalk, talc, fullers earth, kaolin, starch, gums, colloidal silicon dioxide, sodium polyacrylate, tetra alkyl ammonium smectites, trialkyl aryl ammonium smectites, chemically-modified magnesium aluminum silicate, organically-modified Montmorillonite clay, hydrated aluminum silicate, fumed silica, carboxyvinyl polymer, sodium carboxymethyl cellulose, ethylene glycol monostearate, and combinations thereof. The amount of powder(s) in a topical composition is typically 0% to 95%.

The amount of fragrance in a topical composition is typically about 0% to about 0.5%, particularly, about 0.001% to about 0.1%.

Suitable pH adjusting additives include HCl or NaOH in amounts sufficient to adjust the pH of a topical pharmaceutical composition.

The pharmaceutical composition may comprise synthetic oligodeoxynucleotides (ODNs). The synthetic oligonucleotides may comprise unmethylated CpG motifs (CpG ODNs) trigger cells that express Toll-like receptor 9 to mount an innate immune response. CpG ODNs may improve the function of professional antigen-presenting cells. CpG ODNs may boost the generation of humoral and cellular immune responses.

4. METHOD OF TREATING BACTERIAL INFECTION

The disclosed immunogenic proteins and compositions may be used a method of treating a bacterial infection in a subject. For example, the disclosed immunogenic proteins and compositions may be used in a method of treating a Clostridium difficile infection in a subject. The method may comprise administering to a subject in need thereof an immunogenic protein or a composition disclosed herein. The subject may be diagnosed with or at risk of developing a Clostridium difficile infection.

a. Bacterial Infections

The disclosed immunogenic proteins and compositions may be used to treat any bacterial infection in a subject. The disclosed immunogenic proteins and compositions may be administered to a subject who is at risk of developing a bacterial infection or is diagnosed with a bacterial infection. Bacterial infections can affect multiple organs and body systems including, but not limited to, gastrointestinal tract, intestines, skin, mucous membranes, blood, lungs, kidneys, urinary tract, eyes, heart, meninges, respiratory tract, genitals, stomach, bone, connective tissue, and tissue surrounding organs. Bacterial infections may affect more than one organ or body system. Bacterial infections may be systemic. Bacterial infections may be asymptomatic. Bacterial infections may cause a variety of symptoms including, but not limited to, fever, inflammation, wounds that do not heal, weeping wounds, skin rash, red bumps on the skin, abscesses, swollen lymph nodes, nausea, diarrhea, headaches, earaches, sore throat, fatigue, low blood pressure, hyperventilation, weak and rapid pulse, local or systemic pain, and muscle aches. Bacterial infections may cause death. Subjects with co-morbidities or a compromised immune system may be more susceptible to bacterial infections.

The bacterial infection in a subject may be diagnosed prior to treatment with the disclosed immunogenic proteins and compositions. The diagnosis of a bacterial infection may include, but are not limited to, symptomatic diagnostics, microbial culture, microscopy, biochemical tests, PCR based diagnostics, and metagenomics sequencing. A microbial examination may include sample collection, microbial cultivation, identification, and test of antibiotic susceptibility. The diagnosis may include gram staining of the bacterial culture. The diagnosis may include a coagulase test of the bacterial culture. The diagnosis may include a catalase test of the bacterial culture. The diagnosis may include blood tests. The blood tests may include, but are not limited to, a full blood count, measurement of C-reactive protein, measurement of procalcitonin, and measurement of rapid plasma reagin. The diagnosis may include ELISA. The diagnosis may include PCR. The sample may be grown on an agar plate. The sample may be grown in nutrient broth. The growth conditions may include varying factors (e.g., type of growth medium, nutrients, selective compounds, antibiotics, temperature, pH level, oxygen level) to determine the type of bacteria growing. The determination of bacteria growing on an agar plate or in a nutrient broth may determine the bacteria responsible for the subject's infection. Discs containing antibiotic compounds may be placed on the agar plates. The antibiotic compounds may kill the bacteria growing on the plate. The antibiotics that are effective at killing the bacteria may aid in diagnosing the type of bacterial infection.

Samples for diagnosing a bacterial infection may be obtained from the subject in need of treatment. The sample for testing may be from the site of the infection. A sample for testing may be obtained from the subject by swabbing of the skin, throat, or nose. A sample for testing may be obtained from the subject by collecting pus or fluids from wounds, abscesses, or other skin infections. A sample for testing may be obtained from the subject by collecting body fluids. The body fluids may include blood, sputum, urine, and/or other body fluids. Multiple samples may be taken from the subject. Multiple samples may be taken around the site of a prosthesis or medical device.

i. Clostridium difficile

The disclosed immunogenic proteins and compositions may be used to treat a Clostridium difficile infection. The disclosed immunogenic proteins and compositions may be administered to a subject who is at risk of developing a Clostridium difficile infection or is already diagnosed with a Clostridium difficile infection.

Clostridium difficile are anaerobic, motile bacteria, ubiquitous in nature, and especially prevalent in soil. Clostridium difficile infection cells are Gram-positive and show optimum growth on blood agar at human body temperatures in the absence of oxygen. When stressed, the bacteria may produce spores. The Clostridium difficile infection spores may be able to tolerate extreme conditions that the active bacteria cannot tolerate. Pathogenic Clostridium difficile infection strains produce multiple toxins. Clostridium difficile produces toxins. Two Clostridium difficile infection toxins are enterotoxin (Clostridium difficile toxin A (TcdA)) and cytotoxin (Clostridium difficile toxin B (TcdB)). Toxins A and B are glucosyltransferases that target and inactivate the Rho family of GTPases. TcdB may induce actin depolymerization by a mechanism correlated with a decrease in the ADP-ribosylation of the low molecular mass GTP-binding Rho proteins.

Clostridium difficile may be transmitted from person to person by the fecal-oral route. Clostridium difficile may be shed in feces. Any surface, device, or material (e.g., toilets, bathing tubs, and electronic rectal thermometers) that becomes contaminated with feces may serve as a reservoir for the Clostridium difficile spores. Clostridium difficile spores may be transferred to subjects via the hands of healthcare personnel who have touched a contaminated surface or item. Clostridium difficile may live for long periods of time on surfaces. Clostridium difficile spores may be heat-resistant. Clostridium difficile may not be not killed by alcohol-based hand cleansers or routine surface cleaning. Clostridium difficile spores may survive in clinical environments for long periods. Once spores are ingested, their acid-resistance may allow them to pass through the stomach unscathed. The Clostridium difficile spores may germinate and multiply into vegetative cells in the colon upon exposure to bile acids.

Antibiotic therapy for various infections may have the adverse effect of disrupting the normal balance of the gut flora. Clostridium difficile may grow in the presence of an antibiotic. Clostridium difficile may grow in the absence of other bacteria. The growth of Clostridium difficile may cause a Clostridium difficile infection in a subject.

Symptoms of a Clostridium difficile infection may include, but are not limited to watery diarrhea, fever, loss of appetite, nausea, abdominal pain/tenderness. Conditions that may result from a Clostridium difficile infection may include, but are not limited to pseudomembranous colitis (PMC), toxic megacolon, perforations of the colon, sepsis. A Clostridium difficile infection may be deadly. Administration of the disclosed immunogenic proteins or compositions may improve or prevent any one or more symptoms of Clostridium difficile infection.

b. Immunization

Administration of the disclosed immunogenic proteins and compositions comprising the same may immunize the subject against an infection. Immunization may fortify a subject's immune system against an immunogen. A subject may have an immune response in reaction to the presence of an immunogen after immunization with that immunogen. After immunization, the subject may develop the ability to quickly respond to a subsequent encounter with an immunogen because of immunological memory. This may be a function of the adaptive immune system. Therefore, by exposing a subject to an immunogen in a controlled way, the subject's body may protect itself in the presence of an immunogen.

The immunogen may be a Clostridium difficile immunogen. Immunizing a subject with a Clostridium difficile immunogen disclosed herein may prepare the subject's immune system to respond to Clostridium difficile. Immunizing a subject with a Clostridium difficile immunogen may prevent a Clostridium difficile infection. Immunizing a subject with a Clostridium difficile immunogen may treat a Clostridium difficile infection. The Clostridium difficile immunogen may be an immunogen disclosed herein. The Clostridium difficile immunogen may be Tcd169. The Clostridium difficile immunogen may be Tcd169Fl. The Clostridium difficile immunogen may be Tcd138Fl. Clostridium difficile colonization may be targeted. Clostridium difficile growth factors may be targeted. Clostridium difficile toxins may be targeted.

b. Modes of Administration

The disclosed immunogenic proteins or compositions may be administered to the subject by any suitable route. Modes of administration may include tablets, pills, dragees, hard and soft gel capsules, granules, pellets, aqueous, lipid, oily or other solutions, emulsions such as oil-in-water emulsions, liposomes, aqueous or oily suspensions, syrups, elixirs, solid emulsions, solid dispersions or dispersible powders. For the preparation of pharmaceutical compositions for oral administration, the agent may be admixed with commonly known and used adjuvants and excipients such as for example, gum arabic, talcum, starch, sugars (such as, e.g., mannitose, methyl cellulose, lactose), gelatin, surface-active agents, magnesium stearate, aqueous or non-aqueous solvents, paraffin derivatives, cross-linking agents, dispersants, emulsifiers, lubricants, conserving agents, flavoring agents (e.g., ethereal oils), solubility enhancers (e.g., benzyl benzoate or benzyl alcohol) or bioavailability enhancers (e.g. Gelucire®).

For example, the route of administration may include, but is not limited to nasal mucosal, sublingual, oral, subcutaneous, intramuscular, intradermal, or intranasal.

A nasal mucosal route of administration may induce an immune response resulting in systemic and/or mucosal antibody response in a subject. The nasal mucosal route of administration may induce an immune response resulting in intestinal antibody response in a subject. The nasal mucosal route of administration may avoid protein digestion and degradation in the gastrointestinal tract. The nasal mucosal route of administration may require fewer antigens to be delivered than the oral route.

A sublingual route of administration may be used to deliver the disclosed immunogenic proteins and compositions to the bloodstream. The sublingual route of immunization may be easy to deliver. The sublingual route may have the potential for inducing broad systemic and mucosal immune response. The sublingual route of administration may induce intestinal mucosal immunity against infection with enteric pathogens. The sublingual mucosa may encompass the ventral side of the tongue and the floor of the mouth.

Oral administration may be the most effective method of protecting the gut against infection. Oral administration may expose the composition to proteolytic or hydrolyzing digestive enzymes, bile salts, extreme pH, rapid movement of contents, and limited access to the mucosal wall.

The disclosed immunogenic proteins and compositions may be administered to the subject parenterally. For parenteral administration, the immunogenic protein can be dissolved or suspended in a physiologically acceptable diluent, such as, e.g., water, buffer, oils with or without solubilizers, surface-active agents, dispersants or emulsifiers. As oils for example and without limitation, olive oil, peanut oil, cottonseed oil, soybean oil, castor oil and sesame oil may be used. More generally, for parenteral administration, the immunogenic protein or composition can be in the form of an aqueous, lipid, oily or other kind of solution or suspension or even administered in the form of liposomes or nano-suspensions.

c. Combination Therapies

Additional therapeutic agent(s) may be administered simultaneously or sequentially with the disclosed immunogenic proteins and compositions. Sequential administration includes administration before or after the disclosed immunogenic proteins and compositions. In some embodiments, the additional therapeutic agent or agents may be administered in the same composition as the disclosed immunogenic proteins or compositions. In other embodiments, there may be an interval of time between administration of the additional therapeutic agent and the disclosed immunogenic proteins and compositions. In some embodiments, administration of an additional therapeutic agent with a disclosed immunogenic proteins and compositions may allow lower doses of the other therapeutic agents and administration at less frequent intervals. When used in combination with one or more other active ingredients, the immunogenic proteins and compositions of the present invention and the other active ingredients may be used in lower doses than when each is used singly. Accordingly, the immunogenic proteins and compositions of the present invention include those that contain one or more other active ingredients, in addition to immunogenic proteins and compositions. The above combinations include combinations of immunogenic proteins and compositions of the present invention not only with one other active compound, but also with two or more other active compounds.

d. Evaluation of Treatment

The efficacy of the methods of treatment with immunogenic proteins and compositions disclosed herein may be measured. The status of the bacterial infection may be monitored. The efficacy of the methods of treatment disclosed herein may be evaluated by the same or similar methods as used for diagnosis of the bacterial infection.

Evaluating the efficacy of the methods of treatment with the immunogenic proteins, and compositions disclosed herein or monitoring the bacterial infection may include, but are not limited to, symptomatic diagnostics, microbial culture, microscopy, biochemical tests, PCR based tests, and metagenomics sequencing. A microbial examination may include sample collection, microbial cultivation, identification, and test of antibiotic susceptibility. The evaluation or monitoring may include gram staining of the bacterial culture. The evaluation or monitoring may include a coagulase test of the bacterial culture. The evaluation or monitoring may include a catalase test of the bacterial culture. The evaluation or monitoring may include blood tests. The blood tests may include, but are not limited to, a full blood count, measurement of C-reactive protein, measurement of procalcitonin, and measurement of rapid plasma reagin. The evaluation or monitoring may include ELISA. The evaluation or monitoring may include PCR. The sample may be grown on an agar plate. The sample may be grown in nutrient broth. The growth conditions may include varying factors (e.g., type of growth medium, nutrients, selective compounds, antibiotics, temperature, pH level, oxygen level) to determine the type of bacteria growing. The presence, decreased presence, or lack of bacteria growing on an agar plate or in a nutrient broth may determine that the bacterial infection is improving or has been eradicated.

Samples for determining the efficacy of the methods of treatment with the immunogenic proteins, and compositions disclosed herein or monitoring the bacterial infection, may be obtained from the subject. The sample for testing may be from the site of the infection, or the site where the infection was previously present. A sample for testing may be obtained from the subject by swabbing of the skin, throat, or nose. A sample for testing may be obtained from the subject by collecting pus or fluids from wounds, abscesses, or other skin infections. A sample for testing may be obtained from the subject by collecting body fluids. The body fluids may include blood, sputum, urine, and other body fluids. Multiple samples may be taken from the subject. Multiple samples may be taken around the site of a prosthesis or medical device.

The evaluation of the efficacy of methods of treatment with the immunogenic proteins and compositions disclosed herein or monitoring of the bacterial infection may indicate that the subject requires continued treatment with the immunogenic proteins, and compositions disclosed herein. The evaluation of the efficacy of methods of treatment with immunogenic proteins and compositions disclosed herein or monitoring of the bacterial infection may indicate the eradication of the bacterial infection in the subject. The eradication of the bacterial infection may indicate that the subject no longer requires treatment with the immunogenic proteins and compositions disclosed herein.

5. KITS

The immunogenic proteins and compositions may be included in kits comprising the immunogenic proteins and compositions and information, instructions, or both that use of the kit will provide treatment for medical conditions in mammals (particularly humans). The kit may include an additional pharmaceutical composition for use in combination therapy. The kit may include buffers, reagents, or other components to facilitate the mode of administration. The kit may include materials to facilitate nasal mucosal administration. The kit may include materials that facilitate sublingual administration. The information and instructions may be in the form of words, pictures, or both, and the like. In addition or in the alternative, the kit may include the medicament, a composition, or both; and information, instructions, or both, regarding methods of application of medicament, or of composition, preferably with the benefit of treating or preventing medical conditions in mammals (e.g., humans).

The immunogenic proteins and compositions of the invention will be better understood by reference to the following examples, which are intended as an illustration of and not a limitation upon the scope of the invention.

6. EXAMPLES Example 1. Construction of Recombinant Fusion Proteins

As shown in FIG. 1A, TcdA and TcdB share similar domains, including the glucosyltransferase domain (GT), the cysteine proteinase domain (CPD), the transmembrane domain (TMD) and the receptor binding domain (RBD). The DXD motif and a conserved tryptophan in the GT are involved in the enzymatic activity. FIG. 1B shows the construction of Tcd169. Tcd169 was constructed by fusing the GT, CPD, and RBD of TcdB with the RBD of TcdA. The GT and CPD of TcdB are connected without a GGSG linker. The CPD of TcdB is connected to the RBD of TcdB by a GGSG linker (SEQ ID NO: 1), and the RBD of TcdB is connected to the TBD of TcdA by a GGSG linker (SEQ ID NO: 1). Tcd169 lacks a transmembrane domain. Two point mutations, W102A and D288N, were made in the GT of TcdB, and a C689A point mutation was made in the CPD of TcdB. FIG. 1C shows the construction of Tcd169Fl. Tcd169Fl was made by fusing sFliC to Tcd169 with a GGSG linker (SEQ ID NO:1). As such, Tcd169Fl also lacks a transmembrane domain. FIG. 1D shows the construction of Tcd138Fl. Tcd138Fl was made by fusing the GT and CPD of TcdB with the RBD of TcdA, and fusing the RBD of TcdA to sFliC. The GT and CPD of TcdB are connected without a GGSG linker. The CPD of TcdB is connected to the RBC of TcdA by a GGSG linker (SEQ ID NO: 1), and the RBD of TcdA is connected to sFliC by a GGSG linker (SEQ ID NO: 1). Tcd138Fl lacks a transmembrane domain. Two point mutations, W102A and D288N, were made in the GT of TcdB, and a C698A point mutation was made in the CPD of TcdB.

The chimeric DNA encoding the recombinant proteins was ligated into B. megaterium expression vector which adds a C-terminal His-tag to the chimeric proteins. The proteins were subsequently purified from bacterial lysate by Ni-affinity chromatography and gel filtration, and analyzed by SDS-PAGE. FIG. 2 and FIG. 3 show expression and purification of Tcd169 and Tcd169Fl, respectively.

Example 2. Expression of Clostridium difficile Protein Cwp84

To include Cwp84 as a component targeting Clostridium difficile colonization, Cwp84 was expressed and purified using an E. coli expression system. Gene sequence coding for Clostridium difficile Cwp84 was synthesized and cloned into pET21b(+) in E. coli BL21(DE3). Cwp84 protein was purified from bacterial lysate by Ni-affinity chromatography and an ion-exchange fractionation, and analyzed by SDS-PAGE. FIG. 4 shows expression and purification of Cwp84.

Example 3. Rapid Identification of Toxigenic/Non-Toxigenic Clostridium difficile Strains by Multiplex PCR

To rapidly identify toxigenic/non-toxigenic Clostridium difficile strains, a simple and fast 3-plex PCR method was developed to identify tcdA, tcdB and 16s rDNA specific for Clostridium difficile. In this method, 5 μl of 12-24 hrs of Clostridium difficile culture was used as template (FIG. 5). This method will be used to distinguish toxigenic Clostridium difficile strains from non-toxigenic Clostridium difficile strains.

Example 4. Establishment of Novel and More Efficient Mouse Model of Clostridium difficile Toxin Exposure

A mouse model of Clostridium difficile toxin exposure was developed. A 5F infant feeding tube catheter with side ports (Mallinckrodt Inc., St. Louis, Mo.; catalogue no. 85771) was inserted 2.5 cm up the colon. At this point, 100 μl of TcdA (10 μg)+TcdB (10 μg) or PBS was slowly administered over 30 seconds while pressure was applied to the anal area to prevent leakage. Following injection of the solution, the tube was slowly removed and the rectal pressure was maintained for a further 30 seconds. Four hours later, mice were euthanized and dissected to analyze the toxin-mediated effects on the colon. The administration of TcdA/TcdB triggered dramatic colonic inflammation (FIG. 6) and neutrophil and macrophage infiltration. This “intra-rectal toxin instillation” approach may be used to determine immunization protection against toxin challenge via rectum.

Example 5. Tcd169 Immunization Induces Protective Responses Against Both Toxins and Infection with an Epidemic Clostridium difficile Strain

Groups of C57 BL/6 mice (n=10) were immunized with Tcd169 (10 μg) or PBS in the presence of alum for 3 times at 14-day intervals (IM or IP). Immunization with Tcd169 via intraperitoneal (i.p), intramuscular (i.m.) routes induced similar levels of IgG antibody responses against both toxins (FIG. 8A). Tcd169 immunization induced potent neutralizing antibodies against both toxins (FIG. 8B and FIG. 8C). Protection efficacy of Tcd169 immunization was evaluated in a mouse model of CDI. After three immunizations (10 μg Tcd169 per immunization with Alum as adjuvant, at 14-day intervals) via i.p. or i.m. route, mice were challenged with 10⁶ spores of Clostridium difficile UK6 (BI/NAP1/027). In vehicle-immunized mice, significant disease symptoms including weight loss (FIG. 8E) and severe diarrhea in all mice. Approximately 40% of mice succumbed by day 3 (FIG. 8D). In contrast, all Tcd169-immunized mice survived (FIG. 8D) and showed no signs of weight loss (FIG. 8E).

FIG. 9 shows that intramuscular immunization of mice with Tcd169Fl induces potent anti-toxin/sFliC responses. Groups of C57 BL/6 mice (n=10) were immunized with Tcd169Fl (10 μg) or PBS in the presence of alum for 3 times at 14-day intervals (IM). IgG titers against TcdA (FIG. 9A), TcdB (FIG. 9B), or sFliC (FIG. 9C), and IgA titers against TcdA (FIG. 9D), TcdB (FIG. 9E), or sFliC (FIG. 9F) were determined.

FIG. 10 shows that immunization with Tcd169Fl provides mice full protection against infection with hypervirulent Clostridium difficile UK1. Seven days after third immunization with Tcd169Fl, mice were given antibiotic mixture in drinking water for 4 days, switched to regular water for 2 days, and were given one dose of clindamycin (10 mg/kg) one day before infection with 10⁶ of Clostridium difficile UK1 spores by gavage. After infection, mouse survivals (P=0.0486 between PBS and Tcd169Fl) (FIG. 10A), mean relative weight changes (FIG. 10B) and percent diarrhea (FIG. 10C) of different groups were recorded.

Example 6. Determine Antibody Responses and Protection Against Systemic Toxin Challenge in Mice Immunized Intramuscularly with Tcd169Fl or Tcd169Fl and Cwp84 (“Tcd169Fl/Cw”)

Groups of C57BL/6 mice (n=10) aged 6 weeks may be immunized IM with 10 μg of Tcd169Fl or Tcd169Fl and Cwp84 (“Tcd169Fl/Cw”) (10 μg each). Alum may be used as adjuvant for IM immunization. Sera and feces may be collected after each immunization and the anti-toxin, anti-sFliC or anti-Cwp IgA and IgG measured by ELISA.

Example 7. Determine Protection Against Systemic Toxin Challenge

A potent antibody response may be generated, that protects mice against challenge with a lethal dose of TcdA/TcdB (100 ng for each toxin). One week after the third immunization, mice may be challenged IP with a lethal dose of TcdA, TcdB or a mixture of TcdA and TcdB (100 ng for each toxin), and monitored for 72 hrs. If the protection is not optimal, dose optimization experiments may be performed.

Example 8. Optimize Immunization Dose

The initial experiment may use 10 μg of Tcd169Fl and Tcd169Fl/Cw (10 μg each, IM). Dose optimization of the immunogens may follow by doubling and halving the initial immunization dose, and the lowest amount of antigen required to induce the highest level of serum/fecal antibody response for each immunogen may be established.

Example 9. 1d. Challenge the Immunized Mice with Wild-Type Toxins to Determine LD₅₀im (Lethal Dose, 50% Death) for Each Toxin and for the Combination of the Two

One week after the third immunization with optimal dose of Tcd169Fl or Tcd169Fl/Cw, mice may be challenged with doubling doses of 100 ng of TcdA/TcdB or the combination of two. The lethal dose for TcdA/TcdB in mice with body weight around 16-20 g is 100 ng. The dose that causes death of 50% of immunized mice may be determined, and designated as LD₅₀im. The LD₅₀im of each toxin for each immunogen may be determined.

Example 10. Determine the In Vitro Antibody Neutralizing Titers Against Each Toxin, and Determine Anti-Adherence Capability of Antibody Against Adhesion of Clostridium Difficile to Intestinal Epithelial Cells

One week after the third immunization with optimal dose of Tcd169Fl or Tcd169Fl/Cw, sera and feces from each immunized mouse may be collected. Sera or feces from each group may be pooled together. Feces may be dissolved (0.1 g/ml) in PBS containing proteinase inhibitors. Abilities of sera and feces to neutralize the cytotoxicity of TcdA or TcdB may be measured.

The adherence of the Clostridium difficile strains to human colonic enterocyte-like Caco-2 cells may be used to assess in vitro anti-adherence capability of sera and feces. Caco-2 cells in 24-well plates in DMEM may be incubated at 37° C. in 5% CO₂ incubator for 15 days with daily medium change. Overnight Clostridium difficile cultures may be pelleted, washed and resuspended in DMEM, adjusted to 10⁸ cfu/ml. 100 ul of sera or fecal samples (dissolved in PBS) may be added per well, and plates incubated for 1 h. Bacterial suspension (0.5 ml) may then be added to each well (with or without antibody) and plates may then be incubated for 1.5 h at 37° C. under anaerobic conditions. The non-adherent bacteria may be removed by washing five times with PBS and the bound bacteria may be detached by adding 0.5 ml 1% saponin per well. Serial dilutions may be plated on BHI agar plates and colonies may be counted after 48 h of incubation. In parallel, uninfected monolayers (negative control) may be collected by trypsinization, and counted by trypan blue staining in order to express the adherence results as number of viable adherent cfu per one Caco-2 cell. Each adherence assay may be performed in triplicate, and repeated three times.

Example 11. Immunization of Mice

Groups of mice immunized with immunogens 1) lacking adjuvant, or including 2) dmLT or CpG ODNs may be compared. CpG ODNs may be purchased from Invivogen. The outcome of immunization of each immunogen mixed with 5 μg or 10 μg of dmLT or CpG ODNs for IN, SL, and oral immunizations may be compared. Groups of mice may be immunized three times with Tcd169Fl or Tcd169Fl/Cw intranasally (IN), sublingually (SL), or orally. Serum and fecal antibody responses may be measured after each immunization.

Example 12. Routes of Immunization

For Intranasal immunization (IN), 5 μl of Tcd169Fl or Tcd169Fl/Cw with or without adjuvant may be delivered into each nostril (total 10 μl per mouse). The volume of 5 μl per nostril may ensure that all immunogens may be distributed inside of nasal cavity.

For sublingual (SL) immunization, mice may be anesthetized with ketamine/xylazine, and 5 μl of Tcd169Fl or Tcd169Fl/Cw, with or without adjuvant may be delivered at the ventral side of the tongue and directed toward the floor of the mouth.

Example 13. In Vitro Neutralization Titers for Both Systemic and Mucosal Antibodies, and Anti-Adherence Capability of Antibody Against Adhesion of Clostridium difficile to Intestinal Epithelial Cells

The neutralizing titers against TcdA and TcdB, and anti-adherence capability of sera and mucosal samples against adhesion of Clostridium difficile to intestinal epithelial cells may be determined.

Example 14. Protection Against Systemic Challenge of the Toxins

Protection against systemic toxin challenge may be performed. LD₅₀im may be used as the standard challenge dose to assess the levels of the protection against systemic toxin challenge induced by the mucosal immunization for each immunogen. The mucosal immunizations may induce a similar level of protection as do parenteral immunization, in which 50% of mice may survive from challenge with LD₅₀im dose of each wild type toxin, or two toxins given together. Should greater than 50% of mice die, a dose optimization may be performed as described below.

Example 15. Protection Against Mucosal Challenge with Toxins

In the above experiments, the generation of mucosal IgA and IgG antibodies against toxins may be examined. It may be assessed whether these antibodies produced in the gut can protect mice against toxin-mediated destruction of the mucosa. The “intra-rectal toxin instillation” approach may be used.

One week after the third immunization, mice (immunized with immunogens or placebo) may be directly injected with 10 μg of TcdA or TcdB or both (10 μg each) in a volume of 100 μl via rectum. Four hours later, mice may be euthanized and the colon may be carefully removed. Toxin-induced fluid accumulation may be quantitated as the ratio of weight to length. In addition to assessing the fluid accumulation, the pathological signs, such as neutrophil infiltration and villus damage, may be evaluated histologically. Histopathological and neutrophil myeloperoxidase (MPO) activity assays may be performed to evaluate mucosal damage and neutrophil infiltration. The resected colons may be fixed in 4% formaldehyde buffered with PBS and then embedded with paraffin. Deparaffinized 6-μm-thick sections may be stained with haematoxylin and eosin (H&E) for histological analysis, and the tissue injuries may be blindly scored by a histologist. Histological grading criteria may be as follows: 0, minimal infiltration of lymphocytes, plasma cells, and eosinophils; 1+, mild infiltration of lymphocytes, plasma cells, neutrophils, and eosinophils plus mild congestion of the mucosa with or without hyperplasia of gut-associated lymphoid tissue; 2+, moderate infiltrations of mixed inflammatory cells, moderate congestion and edema of the lamina propria, with or without goblet cell hyperplasia, individual surface cell necrosis or vacuolization, and crypt dilatation; 3+, severe inflammation, congestion, edema, and hemorrhage in the mucosa, surface cell necrosis, or degeneration with erosions or ulcers. To measure MPO activities, a portion of the resected colon may be homogenized in 1 ml of 50 mM potassium phosphate buffer with 0.5% hexadecyl trimethyl ammonium bromide and 5 mM EDTA. MPO activities in a centrifuged supernatant may be determined using a substrate o-phenylenediamine in a solution containing 0.05% of H2O2 followed by measuring absorbance at 490 nm.

Example 16. Dose Optimization

Dose optimization of antigens may follow by performing doubling and halving the optimized doses determined in previous examples for 4 immunogens. If an adjuvant is used, e.g. dmLT, the same amount of the adjuvant may be mixed together with the immunogen before injection. For each dose and route of immunization, both systemic and mucosal IgG and IgA response may be monitored and their neutralizing titers may be measured. The lowest amount of antigen required to induce the highest level of serum and mucosal antibody response for each immunogen may be established.

Example 17. Evaluate the Efficacy of the Top-Ranked Regimen of Systemic and Mucosal Immunizations Respectively for Tcd169Fl and Tcd169Fl/Cw in Protecting Mice Against Primary and Recurrent CDI

After 3 immunizations, mice may be pretreated with an antibiotic mixture in drinking water prior to oral challenge with 10⁶ Clostridium difficile UK6 spores. After infection, mice may be monitored for weight loss, diarrhea and modality. Feces may be collected from the day of spore challenge until day 7 post-challenge for counting Clostridium difficile spores and measuring toxin levels. During the period of antibiotic pretreatment, Clostridium difficile challenge and post-infection, mice may be maintained in sterile cages and given sterilized food and water. Cages, food and water may be changed daily until the end of experiments.

For enumeration of Clostridium difficile spore secretion in feces, fecal samples collected from the day of spore challenge until day 7 post-challenge (from both immunized and non-immunized control groups) may be dissolved (0.1 g/ml) in PBS containing proteinase inhibitors, serially diluted to count Clostridium difficile spores. Toxin levels in fecal samples may be determined by ELISA.

Example 18. Protection Against Recurrent CDI in Mice

CDI has become increasingly difficult to manage due, in part, to the ineffectiveness of current antibiotic regimens which are associated with high relapse rates. The efficacy of top-ranked regimens of immunization in preventing disease recurrence in a spore-induced mouse CDI recurrence model which was developed previously may be evaluated. To induce CDI relapse, surviving mice may be given antibiotic cocktail treatment followed by oral gavage of Clostridium difficile UK6 spores (10⁶/mouse) 30 days after the primary infection. The immunization and challenge scheme is illustrated in FIG. 7A. To assess whether immunization also protects against disease relapse in naïve animals that recovered from CDI, surviving mice may be immunized after their recovery from the initial CDI as illustrated (FIG. 8B).

Example 19. Evaluation of the Efficacy of the Top-Ranked Regimen of Systemic and/or Mucosal Immunizations Respectively for Tcd169Fl and Tcd169Fl/Cw, in a Hamster Model of CDI

For IN immunization, 5 μl of Tcd169Fl or Tcd169Fl/Cw, with or without adjuvant may be delivered into each nostril (total 10 μl per mouse). The volume of 5 μl per nostril may ensure that all immunogens may be distributed inside of nasal cavity.

For SL immunization, hamsters may be anesthetized with ketamine/xylazine, and 10 μl of Tcd169Fl or Tcd169Fl/Cw, with or without adjuvant may be delivered at the ventral side of the tongue and directed toward the floor of the mouth.

For oral immunization, 200 μl-400 μl of immunogens may be given to hamsters by gavage.

Example 20. Protection Against CDI in Hamsters

After three immunizations, hamsters may be pretreated with clindamycin followed by challenged with 100 to 10⁴ Clostridium difficile UK6 spores. Weight changes, diarrhea, and modality may be recorded. After infection, fecal samples may be collected for 10 days to compare spore secretion and toxin levels in feces from immunized and non-immunized groups.

It is understood that the foregoing detailed description and accompanying examples are merely illustrative and are not to be taken as limitations upon the scope of the invention, which is defined solely by the appended claims and their equivalents.

Various changes and modifications to the disclosed embodiments may be apparent to those skilled in the art. Such changes and modifications, including without limitation those relating to the chemical structures, substituents, derivatives, intermediates, syntheses, compositions, formulations, or methods of use of the invention, may be made without departing from the spirit and scope thereof.

For reasons of completeness, various aspects of the present disclosure are set out in the following numbered clauses:

Clause 1: An immunogenic protein comprising:

-   -   i) a glucosyltranferase domain of Clostridium difficile toxin         TcdB;     -   ii) a cysteine proteinase domain of Clostridium difficile toxin         TcdB; and     -   iii) a receptor binding domain of Clostridium difficile toxin         TcdA, wherein the immunogenic protein lacks a transmembrane         domain.

Clause 2: The immunogenic protein of clause 1, wherein the immunogenic protein further comprises a receptor binding domain of Clostridium difficile toxin TcdB.

Clause 3: The immunogenic protein of clause 1 or 2, wherein the immunogenic protein further comprises Salmonella typhimurium flagellin.

Clause 4: The immunogenic protein of any one of clauses 1-3, wherein the immunogenic protein further comprises a receptor binding domain of Clostridium difficile toxin TcdB and Salmonella typhimurium flagellin.

Clause 5: The immunogenic protein of any one of clauses 1-4, wherein the glucosyltransferase domain of Clostridium difficile toxin TcdB comprises a W102A amino acid substitution and a D288N amino acid substitution.

Clause 6: The immunogenic protein of any one of clauses 1-5, wherein the cysteine proteinase domain of Clostridium difficile toxin TcdB comprises a C698A amino acid substitution.

Clause 7: A pharmaceutical composition comprising the immunogenic protein of any one of clauses 1-6 and a pharmaceutically acceptable carrier.

Clause 8: A method of treating a Clostridium difficile bacterial infection in a subject in need thereof, the method comprising administering to the subject the immunogenic protein of any one of clauses 1-6 or the pharmaceutical composition of clause 7.

Clause 9: An immunogenic protein comprising:

-   -   i) a glucosyltransferase domain (GT) of Clostridium difficile         toxin TcdB;     -   ii) a cysteine proteinase domain (CPD) of Clostridium difficile         toxin TcdB;     -   iii) a receptor binding domain (RBD) of Clostridium difficile         toxin TcdB; and     -   iv) a receptor binding domain (RBD) of Clostridium difficile         toxin TcdA;     -   wherein the GT of Clostridium difficile toxin TcdB comprises a         W102A amino acid substitution and a D288N amino acid         substitution and the CPD of Clostridium difficile toxin TcdB         comprises a C698A amino acid substitution, and wherein the         immunogenic protein lacks a transmembrane domain.

Clause 10: The immunogenic protein of clause 9 wherein the immunogenic protein comprises the amino acid sequence of SEQ ID NO.: 5.

Clause 11: The immunogenic protein of clause 9 or 10, wherein the immunogenic protein further comprises flagellin of Salmonella typhimurium (sFliC).

Clause 12: The immunogenic protein of clause 11, wherein the immunogenic protein comprises the amino acid sequence of SEQ ID NO.: 6.

Clause 13: A pharmaceutical composition comprising the immunogenic protein of any one of clauses 9-12 and a pharmaceutically acceptable carrier.

Clause 14: A method of treating a Clostridium difficile bacterial infection in a subject in need thereof, the method comprising administering to the subject the immunogenic protein of any one of clauses 9-12 or the pharmaceutical composition of clause 13.

Clause 15: A pharmaceutical composition comprising the immunogenic protein of clause 11 and a Clostridium difficile Cwp84 protein.

Clause 16: A method of treating a Clostridium difficile bacterial infection in a subject in need thereof, the method comprising administering to the subject the pharmaceutical composition of clause 15.

Clause 17: An immunogenic protein comprising:

-   -   i) a glucosyltransferase domain (GT) of Clostridium difficile         toxin TcdB;     -   ii) a cysteine proteinase domain (CPD) of Clostridium difficile         toxin TcdB;     -   iii) a receptor binding domain (RBD) of Clostridium difficile         toxin TcdA; and     -   iv) flagellin of Salmonella typhimurium (sFliC);

wherein the GT of Clostridium difficile toxin TcdB comprises a W102A amino acid substitution and a D288N amino acid substitution and the CPD of Clostridium difficile toxin TcdB comprises a C698A amino acid substitution, and wherein the immunogenic protein lacks a transmembrane domain.

Clause 18: The immunogenic protein of clause 17, wherein the immunogenic protein comprises the amino acid sequence of SEQ ID NO.: 7.

Clause 19: A pharmaceutical composition comprising the immunogenic protein of clause 17 or 18 and a pharmaceutically acceptable carrier.

Clause 20: A method of treating a Clostridium difficile bacterial infection in a subject in need thereof, the method comprising administering to the subject the immunogenic protein of clause 17 or 18 or the pharmaceutical composition of clause 19.

Clause 21: The pharmaceutical composition of any one of clauses 7, 13, or 19, wherein the composition further comprises one or more Clostridium difficile immunogens.

Clause 22: The pharmaceutical composition of clause 21, wherein the one or more Clostridium difficile immunogens is a Cwp84 protein.

Clause 24: A method of treating a Clostridium difficile bacterial infection in a subject in need thereof, the method comprising administering to the subject the pharmaceutical composition of any one of clauses 21-24. 

What is claimed is:
 1. A pharmaceutical composition comprising an immunogenic protein and a Clostridium difficile Cwp84 protein, wherein the immunogenic protein comprises: i) a glucosyltransferase domain (GT) of Clostridium difficile toxin TcdB; ii) a cysteine proteinase domain (CPD) of Clostridium difficile toxin TcdB; iii) a receptor binding domain (RBD) of Clostridium difficile toxin TcdB; iv) a receptor binding domain (RBD) of Clostridium difficile toxin TcdA; and v) flagellin of Salmonella typhimurium (sFliC); wherein the GT of Clostridium difficile toxin TcdB comprises a W102A amino acid substitution and a D288N amino acid substitution when compared to SEQ ID NO.: 8 and the CPD of Clostridium difficile toxin TcdB comprises a C698A amino acid substitution when compared to SEQ ID NO.: 8, and wherein the immunogenic protein lacks a transmembrane domain.
 2. The pharmaceutical composition of claim 1, wherein the GT of Clostridium difficile toxin TcdB is positioned immediately upstream of the CPD of Clostridium difficile toxin TcdB, wherein the amino acid sequence of the linked GT of Clostridium difficile toxin TcdB and the CPD of Clostridium difficile toxin TcdB is set forth in SEQ ID NO.: 8; wherein the RBD of Clostridium difficile toxin TcdA comprises the amino acid sequence of SEQ ID NO.: 9; and wherein the RBD of Clostridium difficile toxin TcdB comprises the amino acid sequence of SEQ ID NO.:
 10. 3. The pharmaceutical composition of claim 1, wherein the RBD of Clostridium difficile toxin TcdA is positioned immediately upstream of sFliC.
 4. The pharmaceutical composition of claim 1, wherein the immunogenic protein comprises the amino acid sequence of SEQ ID NO.:
 6. 5. The pharmaceutical composition of claim 1 further comprising a pharmaceutically acceptable carrier.
 6. The pharmaceutical composition of claim 1 further comprising an adjuvant that is selected from the group consisting of alum, an unmethylated CpG motif, and dmLT.
 7. A method of treating a Clostridium difficile bacterial infection in a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of a pharmaceutical composition that comprises an immunogenic protein and a Clostridium difficile Cwp84 protein, wherein the immunogenic protein comprises: i) a glucosyltransferase domain (GT) of Clostridium difficile toxin TcdB; ii) a cysteine proteinase domain (CPD) of Clostridium difficile toxin TcdB; iii) a receptor binding domain (RBD) of Clostridium difficile toxin TcdB; iv) a receptor binding domain (RBD) of Clostridium difficile toxin TcdA; and v) flagellin of Salmonella typhimurium (sFliC); wherein the GT of Clostridium difficile toxin TcdB comprises a W102A amino acid substitution and a D288N amino acid substitution when compared to SEQ ID NO.: 8 and the CPD of Clostridium difficile toxin TcdB comprises a C698A amino acid substitution when compared to SEQ ID NO.: 8, and wherein the immunogenic protein lacks a transmembrane domain.
 8. The method of claim 7, wherein the GT of Clostridium difficile toxin TcdB is positioned immediately upstream of the CPD of Clostridium difficile toxin TcdB, wherein the amino acid sequence of the linked GT of Clostridium difficile toxin TcdB and the CPD of Clostridium difficile toxin TcdB is set forth in SEQ ID NO.: 8; wherein the RBD of Clostridium difficile toxin TcdA comprises the amino acid sequence of SEQ ID NO.: 9; and wherein the RBD of Clostridium difficile toxin TcdB comprises the amino acid sequence of SEQ ID NO.:
 10. 9. The method of claim 7, wherein the RBD of Clostridium difficile toxin TcdA is positioned immediately upstream of sFliC.
 10. The method of claim 7, wherein the immunogenic protein comprises the amino acid sequence of SEQ ID NO.:
 6. 11. The method of claim 7 further comprising a pharmaceutically acceptable carrier.
 12. The method of claim 7 further comprising an adjuvant that is selected from the group consisting of alum, an unmethylated CpG motif, and dmLT.
 13. A method of treating pseudomembranous colitis or sepsis in a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of a pharmaceutical composition that comprises an immunogenic protein and a Clostridium difficile Cwp84 protein, wherein the immunogenic protein comprises: i) a glucosyltransferase domain (GT) of Clostridium difficile toxin TcdB; ii) a cysteine proteinase domain (CPD) of Clostridium difficile toxin TcdB; iii) a receptor binding domain (RBD) of Clostridium difficile toxin TcdB; iv) a receptor binding domain (RBD) of Clostridium difficile toxin TcdA; and v) flagellin of Salmonella typhimurium (sFliC); wherein the GT of Clostridium difficile toxin TcdB comprises a W102A amino acid substitution and a D288N amino acid substitution when compared to SEQ ID NO.: 8 and the CPD of Clostridium difficile toxin TcdB comprises a C698A amino acid substitution when compared to SEQ ID NO.: 8, and wherein the immunogenic protein lacks a transmembrane domain.
 14. The method of claim 13, wherein the GT of Clostridium difficile toxin TcdB is positioned immediately upstream of the CPD of Clostridium difficile toxin TcdB, wherein the amino acid sequence of the linked GT of Clostridium difficile toxin TcdB and the CPD of Clostridium difficile toxin TcdB is set forth in SEQ ID NO.: 8; wherein the RBD of Clostridium difficile toxin TcdA comprises the amino acid sequence of SEQ ID NO.: 9; and wherein the RBD of Clostridium difficile toxin TcdB comprises the amino acid sequence of SEQ ID NO.:
 10. 15. The method of claim 13, wherein the RBD of Clostridium difficile toxin TcdA is positioned immediately upstream of sFliC.
 16. The method of claim 13, wherein the immunogenic protein comprises the amino acid sequence of SEQ ID NO.:
 6. 17. The method of claim 13 further comprising a pharmaceutically acceptable carrier.
 18. The method of claim 13 further comprising an adjuvant that is selected from the group consisting of alum, an unmethylated CpG motif, and dmLT. 